Sat Oct 8 13:09:53 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 8 2011 at 13:09:53 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3761 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5527779 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -21.53400 35.37600 ymin,ymax (A): -43.70800 20.69400 zmin,zma (A): -12.99700 46.00300 x,y,z range (A): 56.91000 64.40200 59.00000 scale (grids/A): 0.5527779 object centre (A): 6.921001 -11.50700 16.50300 number of atom coordinates read : 3761 total number of charged atoms : 3600 net assigned charge : 6.500016 assigned positive charge : 573.9174 centred at (gu) : 89.83218 91.81972 90.03209 assigned negative charge : -567.4199 centred at (gu) : 89.64286 91.70263 90.00396 start vw surface at 0.1900000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7412 nv = 96 ne = 84 npr = 74595 no. pairs analyzed = 74595 no. exposed pairs = 4849 no. arc points = 34196 no. surface atoms = 1624 nbur = 2137 mkacc time = 0.2500000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 300 mr = 3763 m= 0 mr = 20 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 33 time to turn everything in is 0.5300000 number of dielectric boundary points 3929 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3550 ## 486 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 9812 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9698040E-10 8.1613349E-10 midg,1,midg; midg,igrid,midg -4.9482768E-10 2.7637819E-09 1,midg,midg; igrid,midg,midg -1.6714906E-09 2.4133828E-09 gauss-seidel spectral radius is 0.9831875 estimated iterations to convergence 63 setup time was (sec) 0.8900000 now iterating at: 13:09:54 rms-change max change #iterations 8.9847252E-02 13.23611 at 10iterations 6.1917063E-03 0.8703461 at 20iterations 4.6231921E-04 6.9834709E-02 at 30iterations 4.2578777E-05 9.3154907E-03 at 40iterations 6.1593651E-06 1.6441345E-03 at 50iterations finished qdiffx linear iterations at : 13:09:58 total time elapsed so far: 4.880000 # loops : 50 mean,max change (kT/e) : 6.1593651E-06 1.6441345E-03 energy calculations done at 4.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.120000 DelPhi exited at 13:09:59 5.125u 0.448s 0:05.93 93.7% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 8 2011 at 13:09:59 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3761 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.658334 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -21.53400 35.37600 ymin,ymax (A): -43.70800 20.69400 zmin,zma (A): -12.99700 46.00300 x,y,z range (A): 56.91000 64.40200 59.00000 scale (grids/A): 1.658334 object centre (A): 6.921001 -11.50700 16.50300 number of atom coordinates read : 3761 total number of charged atoms : 3600 net assigned charge : 6.500016 assigned positive charge : 573.9174 centred at (gu) : 89.49538 95.45802 90.09505 assigned negative charge : -567.4199 centred at (gu) : 88.92818 95.10765 90.01153 start vw surface at 0.1900000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 81680 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34196 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 25922 mr = 54623 m= 2915 mr = 17980 m= 103 mr = 1469 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 2118 time to turn everything in is 0.8500000 number of dielectric boundary points 36529 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 468 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 27704 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.5527779 object centre at (A) : 6.921001 -11.50700 16.50300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6122675E-04 2.7229376E-03 midg,1,midg; midg,igrid,midg 1.1739437E-02 5.4722674E-02 1,midg,midg; igrid,midg,midg -7.2591603E-03 3.1894229E-02 gauss-seidel spectral radius is 0.9983262 estimated iterations to convergence 194 setup time was (sec) 1.220000 now iterating at: 13:10:00 rms-change max change #iterations 3.982851 171.8719 at 10iterations 1.711853 62.12616 at 20iterations 0.7366643 23.45188 at 30iterations 0.3188961 10.47386 at 40iterations 0.1372285 4.988899 at 50iterations 5.9233047E-02 1.951935 at 60iterations 2.5537351E-02 0.8282156 at 70iterations 1.1030853E-02 0.3762836 at 80iterations 4.7738426E-03 0.1439571 at 90iterations 2.0656337E-03 6.8586767E-02 at 100iterations 8.9142355E-04 3.1508446E-02 at 110iterations 3.8816273E-04 1.4110565E-02 at 120iterations finished qdiffx linear iterations at : 13:10:13 total time elapsed so far: 13.75000 # loops : 120 mean,max change (kT/e) : 3.8816273E-04 1.4110565E-02 energy calculations done at 13.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.96000 DelPhi exited at 13:10:14 13.966u 0.524s 0:14.79 97.9% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 8 2011 at 13:10:14 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3761 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.487500 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -21.53400 35.37600 ymin,ymax (A): -43.70800 20.69400 zmin,zma (A): -12.99700 46.00300 x,y,z range (A): 56.91000 64.40200 59.00000 scale (grids/A): 2.487500 object centre (A): 6.921001 -11.50700 16.50300 number of atom coordinates read : 3761 total number of charged atoms : 3600 net assigned charge : 6.500016 assigned positive charge : 573.9174 centred at (gu) : 89.24275 98.18676 90.14233 assigned negative charge : -567.4199 centred at (gu) : 88.39212 97.66138 90.01718 start vw surface at 0.2000000 fill in re-entrant regions at 0.6900000 boundary points on vw surface= 189215 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34196 grid for indexing accessible points = 1.400000 m= 88307 mr = 133366 m= 26634 mr = 69695 m= 4621 mr = 20347 m= 385 mr = 3092 m= 5 mr = 197 m= 0 mr = 0 time to grow re-entrant surface = 1.250000 no. cavity mid-points inaccessible to solvent = 7086 time to turn everything in is 2.090000 number of dielectric boundary points 82470 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 2.270000 number of grid points assigned charge 28772 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.658334 object centre at (A) : 6.921001 -11.50700 16.50300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.0991138E-02 5.9415635E-02 midg,1,midg; midg,igrid,midg 0.2963517 0.9321172 1,midg,midg; igrid,midg,midg -0.1584750 0.4620917 gauss-seidel spectral radius is 0.9992045 estimated iterations to convergence 280 setup time was (sec) 2.480000 now iterating at: 13:10:17 rms-change max change #iterations 10.28910 327.4963 at 10iterations 5.944725 156.3755 at 20iterations 3.416250 80.77662 at 30iterations 1.952115 38.59225 at 40iterations 1.109167 26.40755 at 50iterations 0.6305563 13.17114 at 60iterations 0.3575546 7.223119 at 70iterations 0.2020634 4.448267 at 80iterations 0.1142531 2.371700 at 90iterations 6.4455837E-02 1.408796 at 100iterations 3.6401637E-02 0.7902050 at 110iterations 2.0493567E-02 0.4255581 at 120iterations 1.1563562E-02 0.2361469 at 130iterations 6.5255375E-03 0.1363893 at 140iterations 3.6732818E-03 7.1596146E-02 at 150iterations 2.0672362E-03 4.1816711E-02 at 160iterations 1.1634906E-03 2.1329880E-02 at 170iterations 6.5664802E-04 1.3214111E-02 at 180iterations finished qdiffx linear iterations at : 13:10:34 total time elapsed so far: 19.85000 # loops : 180 mean,max change (kT/e) : 6.5664802E-04 1.3214111E-02 energy calculations done at 19.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.05000 DelPhi exited at 13:10:35 20.053u 0.566s 0:20.87 98.7% 0+0k 0+0io 0pf+0w